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!! do_Forces.F90 |
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!! module do_Forces |
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!! Calculates Long Range forces. |
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!! @author Charles F. Vardeman II |
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!! @author Matthew Meineke |
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!! @version $Id: do_Forces.F90,v 1.2 2003-03-06 16:07:55 mmeineke Exp $, $Date: 2003-03-06 16:07:55 $, $Name: not supported by cvs2svn $, $Revision: 1.2 $ |
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!! @version $Id: do_Forces.F90,v 1.9 2003-03-10 23:19:23 gezelter Exp $, $Date: 2003-03-10 23:19:23 $, $Name: not supported by cvs2svn $, $Revision: 1.9 $ |
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module do_Forces |
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use simulation |
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use definitions |
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use generic_atypes |
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use forceGlobals |
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use atype_typedefs |
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use neighborLists |
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|
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|
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use lj_FF |
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use lj |
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use sticky_FF |
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use dp_FF |
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use dipole_dipole |
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use gb_FF |
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#ifdef IS_MPI |
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implicit none |
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PRIVATE |
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|
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!! Number of lj_atypes in lj_atype_list |
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integer, save :: n_atypes = 0 |
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public :: do_force_loop |
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|
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!! Global list of lj atypes in simulation |
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type (atype), pointer :: ListHead => null() |
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type (atype), pointer :: ListTail => null() |
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|
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|
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!! LJ mixing array |
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! type (lj_atype), dimension(:,:), pointer :: ljMixed => null() |
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|
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|
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logical, save :: firstTime = .True. |
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|
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!! Atype identity pointer lists |
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#ifdef IS_MPI |
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!! Row lj_atype pointer list |
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type (identPtrList), dimension(:), pointer :: identPtrListRow => null() |
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!! Column lj_atype pointer list |
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type (identPtrList), dimension(:), pointer :: identPtrListColumn => null() |
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#else |
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type(identPtrList ), dimension(:), pointer :: identPtrList => null() |
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#endif |
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|
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|
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!! Logical has lj force field module been initialized? |
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logical, save :: isFFinit = .false. |
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|
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|
54 |
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!! Public methods and data |
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public :: new_atype |
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public :: do_forceLoop |
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public :: getLjPot |
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public :: init_FF |
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|
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|
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contains |
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|
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!! Adds a new lj_atype to the list. |
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subroutine new_atype(ident,mass,epsilon,sigma, & |
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is_LJ,is_Sticky,is_DP,is_GB,w0,v0,dipoleMoment,status) |
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real( kind = dp ), intent(in) :: mass |
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real( kind = dp ), intent(in) :: epsilon |
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real( kind = dp ), intent(in) :: sigma |
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real( kind = dp ), intent(in) :: w0 |
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real( kind = dp ), intent(in) :: v0 |
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real( kind = dp ), intent(in) :: dipoleMoment |
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|
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integer, intent(in) :: ident |
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integer, intent(out) :: status |
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integer, intent(in) :: is_Sticky |
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integer, intent(in) :: is_DP |
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integer, intent(in) :: is_GB |
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integer, intent(in) :: is_LJ |
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|
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|
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type (atype), pointer :: the_new_atype |
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integer :: alloc_error |
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integer :: atype_counter = 0 |
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integer :: alloc_size |
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integer :: err_stat |
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status = 0 |
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|
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|
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|
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! allocate a new atype |
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allocate(the_new_atype,stat=alloc_error) |
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if (alloc_error /= 0 ) then |
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status = -1 |
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return |
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end if |
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|
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! assign our new atype information |
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the_new_atype%mass = mass |
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the_new_atype%epsilon = epsilon |
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the_new_atype%sigma = sigma |
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the_new_atype%sigma2 = sigma * sigma |
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the_new_atype%sigma6 = the_new_atype%sigma2 * the_new_atype%sigma2 & |
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* the_new_atype%sigma2 |
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the_new_atype%w0 = w0 |
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the_new_atype%v0 = v0 |
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the_new_atype%dipoleMoment = dipoleMoment |
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|
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|
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! assume that this atype will be successfully added |
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the_new_atype%atype_ident = ident |
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the_new_atype%atype_number = n_lj_atypes + 1 |
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|
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if ( is_Sticky /= 0 ) the_new_atype%is_Sticky = .true. |
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if ( is_GB /= 0 ) the_new_atype%is_GB = .true. |
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if ( is_LJ /= 0 ) the_new_atype%is_LJ = .true. |
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if ( is_DP /= 0 ) the_new_atype%is_DP = .true. |
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|
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call add_atype(the_new_atype,ListHead,ListTail,err_stat) |
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if (err_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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|
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n_atypes = n_atypes + 1 |
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|
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|
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end subroutine new_atype |
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|
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|
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subroutine init_FF(nComponents,ident, status) |
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!! Number of components in ident array |
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integer, intent(inout) :: nComponents |
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!! Array of identities nComponents long corresponding to |
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!! ljatype ident. |
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integer, dimension(nComponents),intent(inout) :: ident |
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!! Result status, success = 0, error = -1 |
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integer, intent(out) :: Status |
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|
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integer :: alloc_stat |
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|
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integer :: thisStat |
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integer :: i |
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|
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integer :: myNode |
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#ifdef IS_MPI |
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integer, allocatable, dimension(:) :: identRow |
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integer, allocatable, dimension(:) :: identCol |
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integer :: nrow |
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integer :: ncol |
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#endif |
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status = 0 |
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|
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|
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|
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|
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!! if were're not in MPI, we just update ljatypePtrList |
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#ifndef IS_MPI |
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call create_IdentPtrlst(ident,ListHead,identPtrList,thisStat) |
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if ( thisStat /= 0 ) then |
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status = -1 |
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return |
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endif |
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|
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|
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! if were're in MPI, we also have to worry about row and col lists |
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#else |
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|
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! We can only set up forces if mpiSimulation has been setup. |
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if (.not. isMPISimSet()) then |
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write(default_error,*) "MPI is not set" |
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status = -1 |
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return |
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endif |
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nrow = getNrow(plan_row) |
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ncol = getNcol(plan_col) |
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mynode = getMyNode() |
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!! Allocate temperary arrays to hold gather information |
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allocate(identRow(nrow),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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|
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allocate(identCol(ncol),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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|
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!! Gather idents into row and column idents |
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|
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call gather(ident,identRow,plan_row) |
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call gather(ident,identCol,plan_col) |
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|
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|
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!! Create row and col pointer lists |
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|
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call create_IdentPtrlst(identRow,ListHead,identPtrListRow,thisStat) |
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if (thisStat /= 0 ) then |
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status = -1 |
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return |
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endif |
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|
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call create_IdentPtrlst(identCol,ListHead,identPtrListColumn,thisStat) |
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if (thisStat /= 0 ) then |
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status = -1 |
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return |
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endif |
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|
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!! free temporary ident arrays |
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if (allocated(identCol)) then |
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deallocate(identCol) |
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end if |
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if (allocated(identCol)) then |
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deallocate(identRow) |
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endif |
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|
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#endif |
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|
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call initForce_Modules(thisStat) |
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if (thisStat /= 0) then |
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status = -1 |
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return |
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endif |
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|
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!! Create neighbor lists |
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call expandList(thisStat) |
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if (thisStat /= 0) then |
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status = -1 |
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return |
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endif |
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|
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isFFinit = .true. |
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|
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|
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end subroutine init_FF |
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|
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|
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|
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|
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subroutine initForce_Modules(thisStat) |
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integer, intent(out) :: thisStat |
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integer :: my_status |
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|
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thisStat = 0 |
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call init_lj_FF(ListHead,my_status) |
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if (my_status /= 0) then |
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thisStat = -1 |
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return |
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end if |
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|
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end subroutine initForce_Modules |
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|
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|
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|
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|
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!! FORCE routine Calculates Lennard Jones forces. |
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!! Does force loop over i,j pairs. Calls do_pair to calculates forces. |
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!-------------------------------------------------------------> |
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subroutine do__force_loop(q,A,mu,u_l,f,t,tau,potE,do_pot,FFerror) |
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subroutine do_force_loop(q,A,mu,u_l,f,t,tau,potE,do_pot,FFerror) |
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!! Position array provided by C, dimensioned by getNlocal |
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real ( kind = dp ), dimension(3,getNlocal()) :: q |
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!! Rotation Matrix for each long range particle in simulation. |
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|
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!! Stress Tensor |
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real( kind = dp), dimension(9) :: tau |
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real( kind = dp), dimension(9) :: tauTemp |
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|
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real ( kind = dp ) :: potE |
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logical ( kind = 2) :: do_pot |
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integer :: FFerror |
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real( kind = DP ) :: pot_local |
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|
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!! Local arrays needed for MPI |
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real(kind = dp), dimension(3,getNrow(plan_row)) :: qRow = 0.0_dp |
297 |
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real(kind = dp), dimension(3,getNcol(plan_col)) :: qCol = 0.0_dp |
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|
299 |
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real(kind = dp), dimension(3,getNrow(plan_row)) :: muRow = 0.0_dp |
300 |
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real(kind = dp), dimension(3,getNcol(plan_col)) :: muCol = 0.0_dp |
301 |
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|
302 |
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real(kind = dp), dimension(3,getNrow(plan_row)) :: u_lRow = 0.0_dp |
303 |
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real(kind = dp), dimension(3,getNcol(plan_col)) :: u_lCol = 0.0_dp |
304 |
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|
305 |
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real(kind = dp), dimension(3,getNrow(plan_row)) :: ARow = 0.0_dp |
306 |
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real(kind = dp), dimension(3,getNcol(plan_col)) :: ACol = 0.0_dp |
307 |
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|
308 |
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|
309 |
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|
310 |
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real(kind = dp), dimension(3,getNrow(plan_row)) :: fRow = 0.0_dp |
311 |
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real(kind = dp), dimension(3,getNcol(plan_col)) :: fCol = 0.0_dp |
312 |
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real(kind = dp), dimension(3,getNlocal()) :: fMPITemp = 0.0_dp |
313 |
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|
314 |
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real(kind = dp), dimension(3,getNrow(plan_row)) :: tRow = 0.0_dp |
315 |
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real(kind = dp), dimension(3,getNcol(plan_col)) :: tCol = 0.0_dp |
316 |
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real(kind = dp), dimension(3,getNlocal()) :: tMPITemp = 0.0_dp |
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|
318 |
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|
319 |
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real(kind = dp), dimension(getNrow(plan_row)) :: eRow = 0.0_dp |
320 |
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real(kind = dp), dimension(getNcol(plan_col)) :: eCol = 0.0_dp |
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|
322 |
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real(kind = dp), dimension(getNlocal()) :: eTemp = 0.0_dp |
323 |
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|
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#endif |
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|
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|
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integer :: i, j, jbeg, jend, jnab, idim, jdim, idim2, jdim2, dim, dim2 |
81 |
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integer :: nlist |
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integer :: j_start |
83 |
< |
integer :: tag_i,tag_j |
84 |
< |
real( kind = DP ) :: r, pot, ftmp, dudr, d2, drdx1, kt1, kt2, kt3, ktmp |
85 |
< |
real( kind = dp ) :: fx,fy,fz |
86 |
< |
real( kind = DP ) :: drdx, drdy, drdz |
339 |
< |
real( kind = DP ) :: rxi, ryi, rzi, rxij, ryij, rzij, rijsq |
83 |
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|
84 |
> |
real( kind = DP ) :: r_ij, pot, ftmp, dudr, d2, drdx1, kt1, kt2, kt3, ktmp |
85 |
> |
|
86 |
> |
real( kind = DP ) :: rx_ij, ry_ij, rz_ij, rijsq |
87 |
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real( kind = DP ) :: rlistsq, rcutsq,rlist,rcut |
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|
89 |
< |
real( kind = DP ) :: dielectric = 0.0_dp |
89 |
> |
|
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|
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! a rig that need to be fixed. |
92 |
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#ifdef IS_MPI |
346 |
– |
logical :: newtons_thrd = .true. |
93 |
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real( kind = dp ) :: pe_local |
94 |
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integer :: nlocal |
95 |
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#endif |
122 |
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natoms = getNlocal() |
123 |
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call getRcut(rcut,rcut2=rcutsq) |
124 |
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call getRlist(rlist,rlistsq) |
125 |
+ |
|
126 |
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!! Find ensemble |
127 |
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if (isEnsemble("NPT")) do_stress = .true. |
128 |
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!! set to wrap |
129 |
+ |
if (isPBC()) wrap = .true. |
130 |
|
|
382 |
– |
#ifndef IS_MPI |
383 |
– |
nrow = natoms - 1 |
384 |
– |
ncol = natoms |
385 |
– |
#else |
386 |
– |
nrow = getNrow(plan_row) |
387 |
– |
ncol = getNcol(plan_col) |
388 |
– |
nlocal = natoms |
389 |
– |
j_start = 1 |
390 |
– |
#endif |
131 |
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|
132 |
+ |
|
133 |
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|
134 |
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!! See if we need to update neighbor lists |
135 |
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call check(q,update_nlist) |
395 |
– |
! if (firstTime) then |
396 |
– |
! update_nlist = .true. |
397 |
– |
! firstTime = .false. |
398 |
– |
! endif |
136 |
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|
137 |
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!--------------WARNING........................... |
138 |
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! Zero variables, NOTE:::: Forces are zeroed in C |
139 |
|
! Zeroing them here could delete previously computed |
140 |
|
! Forces. |
141 |
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!------------------------------------------------ |
142 |
< |
#ifndef IS_MPI |
406 |
< |
! nloops = nloops + 1 |
407 |
< |
pe = 0.0E0_DP |
408 |
< |
|
409 |
< |
#else |
410 |
< |
fRow = 0.0E0_DP |
411 |
< |
fCol = 0.0E0_DP |
142 |
> |
call zero_module_variables() |
143 |
|
|
413 |
– |
pe_local = 0.0E0_DP |
144 |
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|
415 |
– |
eRow = 0.0E0_DP |
416 |
– |
eCol = 0.0E0_DP |
417 |
– |
eTemp = 0.0E0_DP |
418 |
– |
#endif |
419 |
– |
|
145 |
|
! communicate MPI positions |
146 |
|
#ifdef IS_MPI |
147 |
< |
call gather(q,qRow,plan_row3d) |
148 |
< |
call gather(q,qCol,plan_col3d) |
147 |
> |
call gather(q,q_Row,plan_row3d) |
148 |
> |
call gather(q,q_Col,plan_col3d) |
149 |
|
|
150 |
< |
call gather(mu,muRow,plan_row3d) |
151 |
< |
call gather(mu,muCol,plan_col3d) |
150 |
> |
call gather(u_l,u_l_Row,plan_row3d) |
151 |
> |
call gather(u_l,u_l_Col,plan_col3d) |
152 |
|
|
153 |
< |
call gather(u_l,u_lRow,plan_row3d) |
154 |
< |
call gather(u_l,u_lCol,plan_col3d) |
430 |
< |
|
431 |
< |
call gather(A,ARow,plan_row_rotation) |
432 |
< |
call gather(A,ACol,plan_col_rotation) |
433 |
< |
|
153 |
> |
call gather(A,A_Row,plan_row_rotation) |
154 |
> |
call gather(A,A_Col,plan_col_rotation) |
155 |
|
#endif |
156 |
|
|
157 |
|
|
437 |
– |
if (update_nlist) then |
438 |
– |
|
439 |
– |
! save current configuration, contruct neighbor list, |
440 |
– |
! and calculate forces |
441 |
– |
call save_neighborList(q) |
442 |
– |
|
443 |
– |
neighborListSize = getNeighborListSize() |
444 |
– |
nlist = 0 |
445 |
– |
|
446 |
– |
|
447 |
– |
|
448 |
– |
do i = 1, nrow |
449 |
– |
point(i) = nlist + 1 |
158 |
|
#ifdef IS_MPI |
451 |
– |
ljAtype_i => identPtrListRow(i)%this |
452 |
– |
tag_i = tagRow(i) |
453 |
– |
rxi = qRow(1,i) |
454 |
– |
ryi = qRow(2,i) |
455 |
– |
rzi = qRow(3,i) |
456 |
– |
#else |
457 |
– |
ljAtype_i => identPtrList(i)%this |
458 |
– |
j_start = i + 1 |
459 |
– |
rxi = q(1,i) |
460 |
– |
ryi = q(2,i) |
461 |
– |
rzi = q(3,i) |
462 |
– |
#endif |
463 |
– |
|
464 |
– |
inner: do j = j_start, ncol |
465 |
– |
#ifdef IS_MPI |
466 |
– |
! Assign identity pointers and tags |
467 |
– |
ljAtype_j => identPtrListColumn(j)%this |
468 |
– |
tag_j = tagColumn(j) |
469 |
– |
if (newtons_thrd) then |
470 |
– |
if (tag_i <= tag_j) then |
471 |
– |
if (mod(tag_i + tag_j,2) == 0) cycle inner |
472 |
– |
else |
473 |
– |
if (mod(tag_i + tag_j,2) == 1) cycle inner |
474 |
– |
endif |
475 |
– |
endif |
476 |
– |
|
477 |
– |
rxij = wrap(rxi - qCol(1,j), 1) |
478 |
– |
ryij = wrap(ryi - qCol(2,j), 2) |
479 |
– |
rzij = wrap(rzi - qCol(3,j), 3) |
480 |
– |
#else |
481 |
– |
ljAtype_j => identPtrList(j)%this |
482 |
– |
rxij = wrap(rxi - q(1,j), 1) |
483 |
– |
ryij = wrap(ryi - q(2,j), 2) |
484 |
– |
rzij = wrap(rzi - q(3,j), 3) |
485 |
– |
|
486 |
– |
#endif |
487 |
– |
rijsq = rxij*rxij + ryij*ryij + rzij*rzij |
488 |
– |
|
489 |
– |
#ifdef IS_MPI |
490 |
– |
if (rijsq <= rlistsq .AND. & |
491 |
– |
tag_j /= tag_i) then |
492 |
– |
#else |
493 |
– |
|
494 |
– |
if (rijsq < rlistsq) then |
495 |
– |
#endif |
496 |
– |
|
497 |
– |
nlist = nlist + 1 |
498 |
– |
if (nlist > neighborListSize) then |
499 |
– |
call expandList(listerror) |
500 |
– |
if (listerror /= 0) then |
501 |
– |
FFerror = -1 |
502 |
– |
write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded." |
503 |
– |
return |
504 |
– |
end if |
505 |
– |
endif |
506 |
– |
list(nlist) = j |
507 |
– |
|
159 |
|
|
160 |
< |
if (rijsq < rcutsq) then |
510 |
< |
|
511 |
< |
r = dsqrt(rijsq) |
160 |
> |
if (update_nlist) then |
161 |
|
|
162 |
< |
call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j) |
162 |
> |
! save current configuration, contruct neighbor list, |
163 |
> |
! and calculate forces |
164 |
> |
call save_neighborList(q) |
165 |
|
|
166 |
< |
#ifdef IS_MPI |
167 |
< |
eRow(i) = eRow(i) + pot*0.5 |
168 |
< |
eCol(i) = eCol(i) + pot*0.5 |
169 |
< |
#else |
170 |
< |
pe = pe + pot |
171 |
< |
#endif |
166 |
> |
neighborListSize = getNeighborListSize() |
167 |
> |
nlist = 0 |
168 |
> |
|
169 |
> |
nrow = getNrow(plan_row) |
170 |
> |
ncol = getNcol(plan_col) |
171 |
> |
nlocal = getNlocal() |
172 |
> |
|
173 |
> |
do i = 1, nrow |
174 |
> |
point(i) = nlist + 1 |
175 |
> |
Atype_i => identPtrListRow(i)%this |
176 |
> |
|
177 |
> |
inner: do j = 1, ncol |
178 |
> |
Atype_j => identPtrListColumn(j)%this |
179 |
|
|
180 |
< |
drdx = -rxij / r |
181 |
< |
drdy = -ryij / r |
182 |
< |
drdz = -rzij / r |
180 |
> |
call get_interatomic_vector(i,j,q_Row(:,i),q_Col(:,j),& |
181 |
> |
rxij,ryij,rzij,rijsq,r) |
182 |
> |
|
183 |
> |
! skip the loop if the atoms are identical |
184 |
> |
if (mpi_cycle_jLoop(i,j)) cycle inner: |
185 |
> |
|
186 |
> |
if (rijsq < rlistsq) then |
187 |
|
|
188 |
< |
fx = dudr * drdx |
527 |
< |
fy = dudr * drdy |
528 |
< |
fz = dudr * drdz |
188 |
> |
nlist = nlist + 1 |
189 |
|
|
190 |
< |
#ifdef IS_MPI |
191 |
< |
fCol(1,j) = fCol(1,j) - fx |
192 |
< |
fCol(2,j) = fCol(2,j) - fy |
193 |
< |
fCol(3,j) = fCol(3,j) - fz |
190 |
> |
if (nlist > neighborListSize) then |
191 |
> |
call expandList(listerror) |
192 |
> |
if (listerror /= 0) then |
193 |
> |
FFerror = -1 |
194 |
> |
write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded." |
195 |
> |
return |
196 |
> |
end if |
197 |
> |
endif |
198 |
|
|
199 |
< |
fRow(1,j) = fRow(1,j) + fx |
536 |
< |
fRow(2,j) = fRow(2,j) + fy |
537 |
< |
fRow(3,j) = fRow(3,j) + fz |
538 |
< |
#else |
539 |
< |
f(1,j) = f(1,j) - fx |
540 |
< |
f(2,j) = f(2,j) - fy |
541 |
< |
f(3,j) = f(3,j) - fz |
542 |
< |
f(1,i) = f(1,i) + fx |
543 |
< |
f(2,i) = f(2,i) + fy |
544 |
< |
f(3,i) = f(3,i) + fz |
545 |
< |
#endif |
199 |
> |
list(nlist) = j |
200 |
|
|
201 |
< |
if (do_stress) then |
202 |
< |
tauTemp(1) = tauTemp(1) + fx * rxij |
203 |
< |
tauTemp(2) = tauTemp(2) + fx * ryij |
550 |
< |
tauTemp(3) = tauTemp(3) + fx * rzij |
551 |
< |
tauTemp(4) = tauTemp(4) + fy * rxij |
552 |
< |
tauTemp(5) = tauTemp(5) + fy * ryij |
553 |
< |
tauTemp(6) = tauTemp(6) + fy * rzij |
554 |
< |
tauTemp(7) = tauTemp(7) + fz * rxij |
555 |
< |
tauTemp(8) = tauTemp(8) + fz * ryij |
556 |
< |
tauTemp(9) = tauTemp(9) + fz * rzij |
201 |
> |
|
202 |
> |
if (rijsq < rcutsq) then |
203 |
> |
call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij) |
204 |
|
endif |
205 |
|
endif |
206 |
|
enddo inner |
207 |
< |
enddo |
207 |
> |
enddo |
208 |
|
|
209 |
< |
#ifdef IS_MPI |
210 |
< |
point(nrow + 1) = nlist + 1 |
211 |
< |
#else |
565 |
< |
point(natoms) = nlist + 1 |
566 |
< |
#endif |
209 |
> |
point(nrow + 1) = nlist + 1 |
210 |
> |
|
211 |
> |
else !! (update) |
212 |
|
|
213 |
< |
else |
213 |
> |
! use the list to find the neighbors |
214 |
> |
do i = 1, nrow |
215 |
> |
JBEG = POINT(i) |
216 |
> |
JEND = POINT(i+1) - 1 |
217 |
> |
! check thiat molecule i has neighbors |
218 |
> |
if (jbeg .le. jend) then |
219 |
|
|
220 |
< |
! use the list to find the neighbors |
221 |
< |
do i = 1, nrow |
222 |
< |
JBEG = POINT(i) |
223 |
< |
JEND = POINT(i+1) - 1 |
224 |
< |
! check thiat molecule i has neighbors |
225 |
< |
if (jbeg .le. jend) then |
226 |
< |
#ifdef IS_MPI |
227 |
< |
ljAtype_i => identPtrListRow(i)%this |
228 |
< |
rxi = qRow(1,i) |
229 |
< |
ryi = qRow(2,i) |
230 |
< |
rzi = qRow(3,i) |
231 |
< |
#else |
582 |
< |
ljAtype_i => identPtrList(i)%this |
583 |
< |
rxi = q(1,i) |
584 |
< |
ryi = q(2,i) |
585 |
< |
rzi = q(3,i) |
586 |
< |
#endif |
587 |
< |
do jnab = jbeg, jend |
588 |
< |
j = list(jnab) |
589 |
< |
#ifdef IS_MPI |
590 |
< |
ljAtype_j = identPtrListColumn(j)%this |
591 |
< |
rxij = wrap(rxi - qCol(1,j), 1) |
592 |
< |
ryij = wrap(ryi - qCol(2,j), 2) |
593 |
< |
rzij = wrap(rzi - qCol(3,j), 3) |
594 |
< |
#else |
595 |
< |
ljAtype_j = identPtrList(j)%this |
596 |
< |
rxij = wrap(rxi - q(1,j), 1) |
597 |
< |
ryij = wrap(ryi - q(2,j), 2) |
598 |
< |
rzij = wrap(rzi - q(3,j), 3) |
599 |
< |
#endif |
600 |
< |
rijsq = rxij*rxij + ryij*ryij + rzij*rzij |
601 |
< |
|
602 |
< |
if (rijsq < rcutsq) then |
220 |
> |
Atype_i => identPtrListRow(i)%this |
221 |
> |
do jnab = jbeg, jend |
222 |
> |
j = list(jnab) |
223 |
> |
Atype_j = identPtrListColumn(j)%this |
224 |
> |
call get_interatomic_vector(i,j,q_Row(:,i),q_Col(:,j),& |
225 |
> |
rxij,ryij,rzij,rijsq,r) |
226 |
> |
|
227 |
> |
call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij) |
228 |
> |
enddo |
229 |
> |
endif |
230 |
> |
enddo |
231 |
> |
endif |
232 |
|
|
604 |
– |
r = dsqrt(rijsq) |
605 |
– |
|
606 |
– |
call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j) |
607 |
– |
#ifdef IS_MPI |
608 |
– |
eRow(i) = eRow(i) + pot*0.5 |
609 |
– |
eCol(i) = eCol(i) + pot*0.5 |
233 |
|
#else |
234 |
< |
pe = pe + pot |
235 |
< |
#endif |
236 |
< |
|
237 |
< |
drdx = -rxij / r |
238 |
< |
drdy = -ryij / r |
239 |
< |
drdz = -rzij / r |
234 |
> |
|
235 |
> |
if (update_nlist) then |
236 |
> |
|
237 |
> |
! save current configuration, contruct neighbor list, |
238 |
> |
! and calculate forces |
239 |
> |
call save_neighborList(q) |
240 |
> |
|
241 |
> |
neighborListSize = getNeighborListSize() |
242 |
> |
nlist = 0 |
243 |
> |
|
244 |
> |
|
245 |
> |
do i = 1, natoms-1 |
246 |
> |
point(i) = nlist + 1 |
247 |
> |
Atype_i => identPtrList(i)%this |
248 |
> |
|
249 |
> |
inner: do j = i+1, natoms |
250 |
> |
Atype_j => identPtrList(j)%this |
251 |
> |
call get_interatomic_vector(i,j,q(:,i),q(:,j),& |
252 |
> |
rxij,ryij,rzij,rijsq,r) |
253 |
> |
|
254 |
> |
if (rijsq < rlistsq) then |
255 |
> |
|
256 |
> |
nlist = nlist + 1 |
257 |
|
|
258 |
< |
fx = dudr * drdx |
259 |
< |
fy = dudr * drdy |
260 |
< |
fz = dudr * drdz |
261 |
< |
|
262 |
< |
#ifdef IS_MPI |
263 |
< |
fCol(1,j) = fCol(1,j) - fx |
264 |
< |
fCol(2,j) = fCol(2,j) - fy |
625 |
< |
fCol(3,j) = fCol(3,j) - fz |
626 |
< |
|
627 |
< |
fRow(1,j) = fRow(1,j) + fx |
628 |
< |
fRow(2,j) = fRow(2,j) + fy |
629 |
< |
fRow(3,j) = fRow(3,j) + fz |
630 |
< |
#else |
631 |
< |
f(1,j) = f(1,j) - fx |
632 |
< |
f(2,j) = f(2,j) - fy |
633 |
< |
f(3,j) = f(3,j) - fz |
634 |
< |
f(1,i) = f(1,i) + fx |
635 |
< |
f(2,i) = f(2,i) + fy |
636 |
< |
f(3,i) = f(3,i) + fz |
637 |
< |
#endif |
638 |
< |
|
639 |
< |
if (do_stress) then |
640 |
< |
tauTemp(1) = tauTemp(1) + fx * rxij |
641 |
< |
tauTemp(2) = tauTemp(2) + fx * ryij |
642 |
< |
tauTemp(3) = tauTemp(3) + fx * rzij |
643 |
< |
tauTemp(4) = tauTemp(4) + fy * rxij |
644 |
< |
tauTemp(5) = tauTemp(5) + fy * ryij |
645 |
< |
tauTemp(6) = tauTemp(6) + fy * rzij |
646 |
< |
tauTemp(7) = tauTemp(7) + fz * rxij |
647 |
< |
tauTemp(8) = tauTemp(8) + fz * ryij |
648 |
< |
tauTemp(9) = tauTemp(9) + fz * rzij |
258 |
> |
if (nlist > neighborListSize) then |
259 |
> |
call expandList(listerror) |
260 |
> |
if (listerror /= 0) then |
261 |
> |
FFerror = -1 |
262 |
> |
write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded." |
263 |
> |
return |
264 |
> |
end if |
265 |
|
endif |
266 |
|
|
267 |
< |
|
267 |
> |
list(nlist) = j |
268 |
> |
|
269 |
> |
|
270 |
> |
if (rijsq < rcutsq) then |
271 |
> |
call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij) |
272 |
> |
endif |
273 |
|
endif |
274 |
< |
enddo |
275 |
< |
endif |
276 |
< |
enddo |
277 |
< |
endif |
278 |
< |
|
274 |
> |
enddo inner |
275 |
> |
enddo |
276 |
> |
|
277 |
> |
point(natoms) = nlist + 1 |
278 |
> |
|
279 |
> |
else !! (update) |
280 |
> |
|
281 |
> |
! use the list to find the neighbors |
282 |
> |
do i = 1, nrow |
283 |
> |
JBEG = POINT(i) |
284 |
> |
JEND = POINT(i+1) - 1 |
285 |
> |
! check thiat molecule i has neighbors |
286 |
> |
if (jbeg .le. jend) then |
287 |
> |
|
288 |
> |
Atype_i => identPtrList(i)%this |
289 |
> |
do jnab = jbeg, jend |
290 |
> |
j = list(jnab) |
291 |
> |
Atype_j = identPtrList(j)%this |
292 |
> |
call get_interatomic_vector(i,j,q(:,i),q(:,j),& |
293 |
> |
rxij,ryij,rzij,rijsq,r) |
294 |
> |
call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij) |
295 |
> |
enddo |
296 |
> |
endif |
297 |
> |
enddo |
298 |
> |
endif |
299 |
|
|
300 |
+ |
#endif |
301 |
|
|
660 |
– |
#ifdef IS_MPI |
661 |
– |
!!distribute forces |
302 |
|
|
303 |
< |
call scatter(fRow,f,plan_row3d) |
304 |
< |
call scatter(fCol,fMPITemp,plan_col3d) |
305 |
< |
|
303 |
> |
#ifdef IS_MPI |
304 |
> |
!! distribute all reaction field stuff (or anything for post-pair): |
305 |
> |
call scatter(rflRow,rflTemp1,plan_row3d) |
306 |
> |
call scatter(rflCol,rflTemp2,plan_col3d) |
307 |
|
do i = 1,nlocal |
308 |
< |
f(1:3,i) = f(1:3,i) + fMPITemp(1:3,i) |
308 |
> |
rflTemp(1:3,i) = rflTemp1(1:3,i) + rflTemp2(1:3,i) |
309 |
|
end do |
310 |
+ |
#endif |
311 |
|
|
312 |
+ |
! This is the post-pair loop: |
313 |
+ |
#ifdef IS_MPI |
314 |
|
|
315 |
< |
call scatter(tRow,t,plan_row3d) |
316 |
< |
call scatter(tCol,tMPITemp,plan_col3d) |
317 |
< |
|
315 |
> |
if (system_has_postpair_atoms) then |
316 |
> |
do i = 1, nlocal |
317 |
> |
Atype_i => identPtrListRow(i)%this |
318 |
> |
call do_postpair(i, Atype_i) |
319 |
> |
enddo |
320 |
> |
endif |
321 |
> |
|
322 |
> |
#else |
323 |
> |
|
324 |
> |
if (system_has_postpair_atoms) then |
325 |
> |
do i = 1, natoms |
326 |
> |
Atype_i => identPtr(i)%this |
327 |
> |
call do_postpair(i, Atype_i) |
328 |
> |
enddo |
329 |
> |
endif |
330 |
> |
|
331 |
> |
#endif |
332 |
> |
|
333 |
> |
|
334 |
> |
#ifdef IS_MPI |
335 |
> |
!!distribute forces |
336 |
> |
|
337 |
> |
call scatter(f_Row,f,plan_row3d) |
338 |
> |
call scatter(f_Col,f_temp,plan_col3d) |
339 |
|
do i = 1,nlocal |
340 |
< |
t(1:3,i) = t(1:3,i) + tMPITemp(1:3,i) |
340 |
> |
f(1:3,i) = f(1:3,i) + f_temp(1:3,i) |
341 |
|
end do |
342 |
|
|
343 |
< |
|
343 |
> |
if (doTorque()) then |
344 |
> |
call scatter(t_Row,t,plan_row3d) |
345 |
> |
call scatter(t_Col,t_temp,plan_col3d) |
346 |
> |
|
347 |
> |
do i = 1,nlocal |
348 |
> |
t(1:3,i) = t(1:3,i) + t_temp(1:3,i) |
349 |
> |
end do |
350 |
> |
endif |
351 |
> |
|
352 |
|
if (do_pot) then |
353 |
|
! scatter/gather pot_row into the members of my column |
354 |
< |
call scatter(eRow,eTemp,plan_row) |
354 |
> |
call scatter(pot_Row, pot_Temp, plan_row) |
355 |
|
|
356 |
|
! scatter/gather pot_local into all other procs |
357 |
|
! add resultant to get total pot |
358 |
|
do i = 1, nlocal |
359 |
< |
pe_local = pe_local + eTemp(i) |
359 |
> |
pot_local = pot_local + pot_Temp(i) |
360 |
|
enddo |
361 |
< |
if (newtons_thrd) then |
362 |
< |
eTemp = 0.0E0_DP |
363 |
< |
call scatter(eCol,eTemp,plan_col) |
364 |
< |
do i = 1, nlocal |
365 |
< |
pe_local = pe_local + eTemp(i) |
366 |
< |
enddo |
367 |
< |
endif |
368 |
< |
pe = pe_local |
361 |
> |
|
362 |
> |
pot_Temp = 0.0_DP |
363 |
> |
|
364 |
> |
call scatter(pot_Col, pot_Temp, plan_col) |
365 |
> |
do i = 1, nlocal |
366 |
> |
pot_local = pot_local + pot_Temp(i) |
367 |
> |
enddo |
368 |
> |
|
369 |
> |
pot = pot_local |
370 |
|
endif |
371 |
|
|
372 |
+ |
if (doStress()) then |
373 |
+ |
mpi_allreduce(tau, tau_Temp,9,mpi_double_precision,mpi_sum, & |
374 |
+ |
mpi_comm_world,mpi_err) |
375 |
+ |
mpi_allreduce(virial, virial_Temp,1,mpi_double_precision,mpi_sum, & |
376 |
+ |
mpi_comm_world,mpi_err) |
377 |
+ |
endif |
378 |
+ |
|
379 |
|
#endif |
380 |
|
|
381 |
< |
potE = pe |
381 |
> |
if (doStress()) then |
382 |
> |
tau = tau_Temp |
383 |
> |
virial = virial_Temp |
384 |
> |
endif |
385 |
|
|
386 |
+ |
end subroutine do_force_loop |
387 |
|
|
388 |
< |
if (do_stress) then |
389 |
< |
#ifdef IS_MPI |
390 |
< |
mpi_allreduce = (tau,tauTemp,9,mpi_double_precision,mpi_sum, & |
391 |
< |
mpi_comm_world,mpi_err) |
388 |
> |
|
389 |
> |
!! Calculate any pre-force loop components and update nlist if necessary. |
390 |
> |
subroutine do_preForce(updateNlist) |
391 |
> |
logical, intent(inout) :: updateNlist |
392 |
> |
|
393 |
> |
|
394 |
> |
|
395 |
> |
end subroutine do_preForce |
396 |
> |
|
397 |
> |
|
398 |
> |
|
399 |
> |
|
400 |
> |
|
401 |
> |
|
402 |
> |
|
403 |
> |
|
404 |
> |
|
405 |
> |
|
406 |
> |
|
407 |
> |
|
408 |
> |
|
409 |
> |
!! Calculate any post force loop components, i.e. reaction field, etc. |
410 |
> |
subroutine do_postForce() |
411 |
> |
|
412 |
> |
|
413 |
> |
|
414 |
> |
end subroutine do_postForce |
415 |
> |
|
416 |
> |
|
417 |
> |
|
418 |
> |
|
419 |
> |
|
420 |
> |
|
421 |
> |
|
422 |
> |
|
423 |
> |
|
424 |
> |
|
425 |
> |
|
426 |
> |
|
427 |
> |
|
428 |
> |
|
429 |
> |
|
430 |
> |
|
431 |
> |
|
432 |
> |
subroutine do_pair(atype_i,atype_j,i,j,r_ij,rx_ij,ry_ij,rz_ij) |
433 |
> |
type (atype ), pointer, intent(inout) :: atype_i |
434 |
> |
type (atype ), pointer, intent(inout) :: atype_j |
435 |
> |
integer :: i |
436 |
> |
integer :: j |
437 |
> |
real ( kind = dp ), intent(inout) :: rx_ij |
438 |
> |
real ( kind = dp ), intent(inout) :: ry_ij |
439 |
> |
real ( kind = dp ), intent(inout) :: rz_ij |
440 |
> |
|
441 |
> |
|
442 |
> |
real( kind = dp ) :: fx = 0.0_dp |
443 |
> |
real( kind = dp ) :: fy = 0.0_dp |
444 |
> |
real( kind = dp ) :: fz = 0.0_dp |
445 |
> |
|
446 |
> |
real( kind = dp ) :: drdx = 0.0_dp |
447 |
> |
real( kind = dp ) :: drdy = 0.0_dp |
448 |
> |
real( kind = dp ) :: drdz = 0.0_dp |
449 |
> |
|
450 |
> |
|
451 |
> |
#ifdef IS_MPI |
452 |
> |
|
453 |
> |
if (Atype_i%is_LJ .and. Atype_j%is_LJ) then |
454 |
> |
call do_lj_pair(i, j, atype_i, atype_j, rx_ij, ry_ij, rz_ij, r_ij, & |
455 |
> |
pot, f) |
456 |
> |
endif |
457 |
> |
|
458 |
> |
if (Atype_i%is_dp .and. Atype_j%is_dp) then |
459 |
> |
|
460 |
> |
call do_dipole_pair(i, j, atype_i, atype_j, rx_ij, ry_ij, rz_ij, r_ij, & |
461 |
> |
rt, rrf, pot, u_l, f, t) |
462 |
> |
|
463 |
> |
if (do_reaction_field) then |
464 |
> |
call accumulate_rf(i, j, r_ij, rt, rrf) |
465 |
> |
endif |
466 |
> |
|
467 |
> |
endif |
468 |
> |
|
469 |
> |
if (Atype_i%is_sticky .and. Atype_j%is_sticky) then |
470 |
> |
call getstickyforce(r, pot, dudr, Atype_i, Atype_j) |
471 |
> |
endif |
472 |
> |
|
473 |
|
#else |
474 |
< |
tau = tauTemp |
475 |
< |
#endif |
474 |
> |
|
475 |
> |
if (Atype_i%is_LJ .and. Atype_j%is_LJ) then |
476 |
> |
call do_lj_pair(i, j, atype_i, atype_j, rx_ij, ry_ij, rz_ij, r_ij, & |
477 |
> |
pot, f) |
478 |
|
endif |
479 |
|
|
480 |
+ |
if (Atype_i%is_dp .and. Atype_j%is_dp) then |
481 |
+ |
call do_dipole_pair(i, j, atype_i, atype_j, rx_ij, ry_ij, rz_ij, r_ij, & |
482 |
+ |
rt, rrf, pot, u_l, f, t) |
483 |
|
|
484 |
< |
end subroutine do_force_loop |
484 |
> |
if (do_reaction_field) then |
485 |
> |
call accumulate_rf(i, j, r_ij, rt, rrf) |
486 |
> |
endif |
487 |
|
|
488 |
+ |
endif |
489 |
|
|
490 |
+ |
if (Atype_i%is_sticky .and. Atype_j%is_sticky) then |
491 |
+ |
call getstickyforce(r,pot,dudr, Atype_i, Atype_j) |
492 |
+ |
endif |
493 |
|
|
494 |
+ |
#endif |
495 |
+ |
|
496 |
+ |
|
497 |
+ |
end subroutine do_pair |
498 |
+ |
|
499 |
+ |
|
500 |
+ |
|
501 |
+ |
|
502 |
+ |
|
503 |
+ |
|
504 |
+ |
|
505 |
+ |
|
506 |
+ |
|
507 |
+ |
|
508 |
+ |
|
509 |
+ |
|
510 |
+ |
|
511 |
+ |
|
512 |
+ |
|
513 |
+ |
|
514 |
+ |
subroutine get_interatomic_vector(q_i,q_j,rx_ij,ry_ij,rz_ij,r_sq,r_ij) |
515 |
+ |
!---------------- Arguments------------------------------- |
516 |
+ |
!! index i |
517 |
+ |
|
518 |
+ |
!! Position array |
519 |
+ |
real (kind = dp), dimension(3) :: q_i |
520 |
+ |
real (kind = dp), dimension(3) :: q_j |
521 |
+ |
!! x component of vector between i and j |
522 |
+ |
real ( kind = dp ), intent(out) :: rx_ij |
523 |
+ |
!! y component of vector between i and j |
524 |
+ |
real ( kind = dp ), intent(out) :: ry_ij |
525 |
+ |
!! z component of vector between i and j |
526 |
+ |
real ( kind = dp ), intent(out) :: rz_ij |
527 |
+ |
!! magnitude of r squared |
528 |
+ |
real ( kind = dp ), intent(out) :: r_sq |
529 |
+ |
!! magnitude of vector r between atoms i and j. |
530 |
+ |
real ( kind = dp ), intent(out) :: r_ij |
531 |
+ |
!! wrap into periodic box. |
532 |
+ |
logical, intent(in) :: wrap |
533 |
+ |
|
534 |
+ |
!--------------- Local Variables--------------------------- |
535 |
+ |
!! Distance between i and j |
536 |
+ |
real( kind = dp ) :: d(3) |
537 |
+ |
!---------------- END DECLARATIONS------------------------- |
538 |
+ |
|
539 |
+ |
|
540 |
+ |
! Find distance between i and j |
541 |
+ |
d(1:3) = q_i(1:3) - q_j(1:3) |
542 |
+ |
|
543 |
+ |
! Wrap back into periodic box if necessary |
544 |
+ |
if ( wrap ) then |
545 |
+ |
d(1:3) = d(1:3) - thisSim%box(1:3) * sign(1.0_dp,thisSim%box(1:3)) * & |
546 |
+ |
int(abs(d(1:3)/thisSim%box(1:3) + 0.5_dp) |
547 |
+ |
end if |
548 |
+ |
|
549 |
+ |
! Find Magnitude of the vector |
550 |
+ |
r_sq = dot_product(d,d) |
551 |
+ |
r_ij = sqrt(r_sq) |
552 |
+ |
|
553 |
+ |
! Set each component for force calculation |
554 |
+ |
rx_ij = d(1) |
555 |
+ |
ry_ij = d(2) |
556 |
+ |
rz_ij = d(3) |
557 |
+ |
|
558 |
+ |
|
559 |
+ |
end subroutine get_interatomic_vector |
560 |
+ |
|
561 |
+ |
subroutine zero_module_variables() |
562 |
+ |
|
563 |
+ |
#ifndef IS_MPI |
564 |
+ |
|
565 |
+ |
pe = 0.0E0_DP |
566 |
+ |
tauTemp = 0.0_dp |
567 |
+ |
fTemp = 0.0_dp |
568 |
+ |
tTemp = 0.0_dp |
569 |
+ |
#else |
570 |
+ |
qRow = 0.0_dp |
571 |
+ |
qCol = 0.0_dp |
572 |
+ |
|
573 |
+ |
muRow = 0.0_dp |
574 |
+ |
muCol = 0.0_dp |
575 |
+ |
|
576 |
+ |
u_lRow = 0.0_dp |
577 |
+ |
u_lCol = 0.0_dp |
578 |
+ |
|
579 |
+ |
ARow = 0.0_dp |
580 |
+ |
ACol = 0.0_dp |
581 |
+ |
|
582 |
+ |
fRow = 0.0_dp |
583 |
+ |
fCol = 0.0_dp |
584 |
+ |
|
585 |
+ |
|
586 |
+ |
tRow = 0.0_dp |
587 |
+ |
tCol = 0.0_dp |
588 |
+ |
|
589 |
+ |
|
590 |
+ |
|
591 |
+ |
eRow = 0.0_dp |
592 |
+ |
eCol = 0.0_dp |
593 |
+ |
eTemp = 0.0_dp |
594 |
+ |
#endif |
595 |
+ |
|
596 |
+ |
end subroutine zero_module_variables |
597 |
+ |
|
598 |
+ |
|
599 |
+ |
!! Function to properly build neighbor lists in MPI using newtons 3rd law. |
600 |
+ |
!! We don't want 2 processors doing the same i j pair twice. |
601 |
+ |
!! Also checks to see if i and j are the same particle. |
602 |
+ |
function checkExcludes(atom1,atom2) result(do_cycle) |
603 |
+ |
!--------------- Arguments-------------------------- |
604 |
+ |
! Index i |
605 |
+ |
integer,intent(in) :: atom1 |
606 |
+ |
! Index j |
607 |
+ |
integer,intent(in), optional :: atom2 |
608 |
+ |
! Result do_cycle |
609 |
+ |
logical :: do_cycle |
610 |
+ |
!--------------- Local variables-------------------- |
611 |
+ |
integer :: tag_i |
612 |
+ |
integer :: tag_j |
613 |
+ |
integer :: i |
614 |
+ |
!--------------- END DECLARATIONS------------------ |
615 |
+ |
do_cycle = .false. |
616 |
+ |
|
617 |
+ |
#ifdef IS_MPI |
618 |
+ |
tag_i = tagRow(atom1) |
619 |
+ |
#else |
620 |
+ |
tag_i = tag(atom1) |
621 |
+ |
#endif |
622 |
+ |
|
623 |
+ |
!! Check global excludes first |
624 |
+ |
if (.not. present(atom2)) then |
625 |
+ |
do i = 1,nGlobalExcludes |
626 |
+ |
if (excludeGlobal(i) == tag_i) then |
627 |
+ |
do_cycle = .true. |
628 |
+ |
return |
629 |
+ |
end if |
630 |
+ |
end do |
631 |
+ |
return !! return after checking globals |
632 |
+ |
end if |
633 |
+ |
|
634 |
+ |
!! we return if j not present here. |
635 |
+ |
tag_j = tagColumn(j) |
636 |
+ |
|
637 |
+ |
|
638 |
+ |
|
639 |
+ |
if (tag_i == tag_j) then |
640 |
+ |
do_cycle = .true. |
641 |
+ |
return |
642 |
+ |
end if |
643 |
+ |
|
644 |
+ |
if (tag_i < tag_j) then |
645 |
+ |
if (mod(tag_i + tag_j,2) == 0) do_cycle = .true. |
646 |
+ |
return |
647 |
+ |
else |
648 |
+ |
if (mod(tag_i + tag_j,2) == 1) do_cycle = .true. |
649 |
+ |
endif |
650 |
+ |
|
651 |
+ |
|
652 |
+ |
|
653 |
+ |
do i = 1, nLocalExcludes |
654 |
+ |
if (tag_i = excludes(1,i) .and. excludes(2,i) < 0) then |
655 |
+ |
do_cycle = .true. |
656 |
+ |
return |
657 |
+ |
end if |
658 |
+ |
end do |
659 |
+ |
|
660 |
+ |
|
661 |
+ |
end function checkExcludes |
662 |
+ |
|
663 |
+ |
|
664 |
|
end module do_Forces |